Contacts of the helix formed by residues 9 - 19 (chain C) in PDB entry 1C04
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 9 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C THR 3.0 6.5 - - - +
8C PRO* 1.3 86.5 - - + +
10C ALA* 1.3 65.5 + - - +
11C ALA 3.2 0.3 + - - -
12C VAL* 3.2 15.4 + - + -
13C LEU* 2.9 18.9 + - - +
47C LYS* 3.5 9.2 - - - +
10E U 4.7 10.3 - - + +
11E A 4.7 9.6 - - - +
12E G 2.7 13.2 - - - +
13E G 1.6 38.8 - - - +
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Residues in contact with ALA 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PRO 3.6 0.6 + - - -
9C PRO* 1.3 72.1 - - - +
11C ALA* 1.3 54.3 + - - +
13C LEU* 3.1 10.1 + - - +
14C LEU* 2.7 44.0 + - + +
43C ILE* 5.2 0.2 - - - -
47C LYS* 3.9 8.6 - - + +
63C ILE* 3.9 23.6 - - + -
66C THR* 3.7 24.9 - - - +
10E U 4.7 9.3 - - - +
12E G 3.6 12.0 + - - +
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Residues in contact with ALA 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ALA* 1.3 79.9 - - - +
12C VAL* 1.3 60.7 + - - -
14C LEU* 3.0 2.6 + - - +
15C LYS* 2.8 22.3 + - - +
66C THR* 4.2 1.5 - - - +
70C MET* 4.2 6.2 - - - +
12E G 3.4 2.2 + - - -
13E G 0.7 108.6 + - - +
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Residues in contact with VAL 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PRO* 4.2 11.7 - - + -
9C PRO* 3.3 36.6 - - + +
11C ALA* 1.3 75.3 - - - +
13C LEU* 1.3 64.2 + - - +
15C LYS* 2.9 4.3 + - + +
16C LYS* 2.9 29.5 + - + +
13E G 3.1 8.2 + - - +
14E C 3.6 19.1 - - - +
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PRO* 3.1 38.6 - - + +
9C PRO 2.9 8.6 + - - +
10C ALA* 3.4 8.1 - - - +
12C VAL* 1.3 77.1 - - + +
14C LEU* 1.3 53.3 + - - +
16C LYS* 3.3 9.9 + - + +
17C ALA* 2.8 35.3 + - - +
43C ILE* 3.3 39.3 - - + +
46C LEU* 3.8 30.3 - - + -
47C LYS* 3.9 18.2 - - + -
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ALA 2.7 22.0 + - - +
11C ALA 3.4 4.5 - - - +
13C LEU* 1.3 69.9 - - - +
15C LYS* 1.3 56.7 + - - +
17C ALA* 4.0 5.2 - - + -
18C ALA* 2.6 39.0 + - - +
34C THR* 5.2 6.7 - - + -
40C VAL* 5.0 9.4 - - + -
43C ILE* 3.9 20.2 - - + -
63C ILE* 3.6 22.7 - - + +
66C THR* 3.9 10.3 - - - -
67C ALA* 3.4 47.1 - - + +
70C MET* 4.1 10.5 - - - -
72C ILE* 4.5 11.9 - - + -
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ALA 2.8 11.2 + - - +
12C VAL* 2.9 9.2 + - + +
14C LEU* 1.3 75.1 - - - +
16C LYS* 1.3 54.5 + - - +
18C ALA* 3.7 0.7 - - - +
19C GLY 2.7 31.2 + - - -
20C ILE* 3.0 35.4 + - + +
21C GLU* 2.7 33.3 + - - +
22C SER* 3.3 0.8 - - - +
70C MET* 3.8 12.3 - - + +
13E G 2.9 4.9 - - - +
14E C 1.2 98.0 + - - +
15E U 3.2 5.2 + - - -
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Residues in contact with LYS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 2.9 19.9 + - + +
13C LEU* 3.7 10.8 - - + +
15C LYS* 1.3 74.3 - - - +
17C ALA* 1.3 68.5 + - - +
19C GLY* 3.7 7.3 + - - -
20C ILE 5.0 2.0 - - - +
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Residues in contact with ALA 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU 2.8 17.8 + - - +
14C LEU* 3.5 7.0 - - + +
16C LYS* 1.3 78.2 - - - +
18C ALA* 1.3 68.6 + - - +
19C GLY* 2.8 3.8 + - - -
34C THR* 4.4 12.4 + - + +
39C LYS* 4.4 23.0 - - + +
43C ILE* 3.8 22.2 - - + -
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU 2.6 23.4 + - - +
15C LYS 3.7 2.5 - - - +
17C ALA* 1.3 72.7 - - - +
19C GLY* 1.3 58.1 + - - +
20C ILE* 4.2 6.1 - - + -
32C VAL* 3.3 38.3 - - + +
33C ALA 4.2 3.1 - - - +
34C THR* 4.3 12.9 + - + +
72C ILE* 3.6 25.6 - - + -
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Residues in contact with GLY 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LYS 2.7 12.9 + - - -
16C LYS* 4.1 6.3 - - - -
17C ALA 2.8 6.2 + - - -
18C ALA* 1.3 75.1 - - - +
20C ILE* 1.3 67.7 + - - +
32C VAL* 5.0 1.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il